Bioconductor Forum

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DEP

updated 6 days ago by shepherl 3.8k • written 7 days ago by Namrata • 0

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qvalue

updated 3 days ago by James W. MacDonald 65k • written 5 days ago by John • 0

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scran BiocParallel bluster

1 day ago • updated 8 hours ago ATpoint ★ 4.0k

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DESeq2 RNAseq

updated 19 hours ago by Michael Love 41k • written 22 hours ago by kcarey • 0

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edgeR

updated 1 day ago by Gordon Smyth 50k • written 1 day ago by k___ ▴ 30

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 1 hour ago by James W. MacDonald 65k • written 3 hours ago by Alexandre • 0

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ASpli

5 days ago Sebashish • 0

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 1 day ago by James W. MacDonald 65k • written 2 days ago by fernanda.backsouza ▴ 10

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RNAseq123

3 days ago Lluís Revilla Sancho ▴ 730

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levi NURSFPX ragene20sttranscriptcluster.db ssrch

4 days ago vaxahey107 • 0

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DESeq2 PCAtools

updated 1 hour ago by JKim • 0 • written 12 hours ago by Aaliya • 0

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Rsubread

1 day ago Dario Strbenac ★ 1.5k

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tidySpatialExperiment SpatialExperiment MoleculeExperiment

2 days ago info ▴ 10

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GDCRNATools TCGA

8 hours ago glaciya2018 • 0

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DiffBind

23 hours ago • updated 22 hours ago Shloka • 0

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DEXSeq SGSeq

1 day ago Sara • 0

67 results • Page 2 of 2

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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0